Fix retrieval of phenotypes by well, add options for retrieving wells by compound.

R/PhenotypeHandle.R

@@ -34,7 +34,7 @@ PhenotypeHandle <- R6Class(
     #' @param well A Well object
     #' @return List of Phenotype objects
     get_all_by_well = function(well) {
-      query <- "SELECT P.* FROM Phenotype AS P, Well_has_Phenotype AS WhP
+      query <- "SELECT P.*, WhP.value, WhP.unit FROM Phenotype AS P, Well_has_Phenotype AS WhP
                 WHERE WhP.Plate_ID = ? AND WhP.Well_position = ? AND
                       WhP.Phenotype_ID = P.ID"
       data <- self$dbConnection$get_data(query, list(well$plate_ID, well$position))
@@ -47,7 +47,9 @@ PhenotypeHandle <- R6Class(
                               xrefID = df$xrefID, 
                               xrefDB = df$xrefDB,
                               name = df$name,
-                              description = df$description)
+                              description = df$description,
+                              value = df$value,
+                              unit = df$unit)
           phenotypes <- c(phenotypes, ph)
         }
         return(phenotypes)

R/ScreenHandle.R

@@ -110,7 +110,7 @@ ScreenHandle <- R6Class(
     #' @description Store Screen objects in the database
     #' @param screen.list A list of Screen objects
     #' @param fast.mode (optional, default: FALSE) Speeds up data loading by
-    #' disabling integrity checks
+    #' disabling integrity checks.
     store = function(screen.list, fast.mode = FALSE) {
       if(fast.mode) { # Disable integrity checks
         result <- self$dbConnection$execute("SET @@session.unique_checks = 0")

R/WellHandle.R

@@ -95,21 +95,42 @@ WellHandle <- R6Class(
     #' @description Retrieve all wells where a compound is found
     #' @param compound A Compound object
     #' @param screen (optional) a Screen object to limit to wells from this screen
+    #' @param dose (optional) limit to wells with this dose. Unit must also be specified.
+    #' @param unit (optional) unit for the dose value.
     #' @return List of Well objects
-    get_all_by_compound = function(compound, screen = NULL) {
+    get_all_by_compound = function(compound, screen = NULL, dose = NULL, unit = NULL) {
       if(is.null(screen)) {
-        query <- "SELECT W.* FROM Well AS W, Well_has_Compound AS WhC
-                  WHERE WhC.Compound_ID = ?
-                  AND WhC.Plate_ID = W.Plate_ID
-                  AND WhC.Well_position = W.position"
-        data <- self$dbConnection$get_data(query, list(compound$ID))
+        if(is.null(dose) || is.null(unit)) {
+          query <- "SELECT W.* FROM Well AS W, Well_has_Compound AS WhC
+                    WHERE WhC.Compound_ID = ?
+                    AND WhC.Plate_ID = W.Plate_ID
+                    AND WhC.Well_position = W.position"
+          data <- self$dbConnection$get_data(query, list(compound$ID))
+        } else {
+          query <- "SELECT W.* FROM Well AS W, Well_has_Compound AS WhC
+                    WHERE WhC.Compound_ID = ?
+                    AND WhC.Plate_ID = W.Plate_ID
+                    AND WhC.Well_position = W.position
+                    AND WhC.dose = ? AND lower(WhC.unit) = ?"
+          data <- self$dbConnection$get_data(query, list(compound$ID, dose, tolower(unit)))
+        }
       } else {
-        query <- "SELECT W.* FROM Well AS W, Well_has_Compound AS WhC, Screen_has_Plate AS ShP
-                  WHERE WhC.Compound_ID = ? AND ShP.Screen_ID = ?
-                  AND ShP.Plate_ID = WhC.Plate_ID
-                  AND WhC.Plate_ID = W.Plate_ID
-                  AND WhC.Well_position = W.position" 
-        data <- self$dbConnection$get_data(query, list(compound$ID, screen$ID))
+        if(is.null(dose) || is.null(unit)) {
+          query <- "SELECT W.* FROM Well AS W, Well_has_Compound AS WhC, Screen_has_Plate AS ShP
+                    WHERE WhC.Compound_ID = ? AND ShP.Screen_ID = ?
+                    AND ShP.Plate_ID = WhC.Plate_ID
+                    AND WhC.Plate_ID = W.Plate_ID
+                    AND WhC.Well_position = W.position" 
+          data <- self$dbConnection$get_data(query, list(compound$ID, screen$ID))
+        } else {
+          query <- "SELECT W.* FROM Well AS W, Well_has_Compound AS WhC, Screen_has_Plate AS ShP
+                    WHERE WhC.Compound_ID = ? AND ShP.Screen_ID = ?
+                    AND ShP.Plate_ID = WhC.Plate_ID
+                    AND WhC.Plate_ID = W.Plate_ID
+                    AND WhC.Well_position = W.position
+                    AND WhC.dose = ? AND lower(WhC.unit) = ?" 
+          data <- self$dbConnection$get_data(query, list(compound$ID, screen$ID, dose, tower(unit))
+  )      }
       }
       if(length(data$position)>0) {
         wells <- list()